Body measurement traits, influenced by genes and environmental factors, play numerous important roles in the value assessment of productivity and economy. Growth differentiate factor 5 (GDF5), involved in the development and maintenance of bone and cartilage, is an important candidate gene for body measurement traits selection through marker-assisted selection (MAS). In this study, based on the PCR-RFLP technology, we discovered and evaluated the potential association of the single nucleotide polymorphism (SNP) (T586C in exon 1) of the bovine GDF5 gene with body measurement traits in 985 Bos taurus breed, 42 Bos indicus breed and 76 Bos indicus x Bos taurus individuals. As the SNP marker, there were the significant effects on the Body length (BL) in the Bos taurus (BT) and Bos indicus x Bos taurus (BMY) populations (P < 0.05). In BT population, animals with the genotype TT had lower mean values for BL and Hip width (HW) than these with the TC and CC genotype (P < 0.01). In BMY population, animals with the genotype TC had lower mean values for BL than these with the genotype CC (P < 0.05). These results suggest that the SNP of the GDF5 gene could be a very useful genetic marker for body measurement traits in the bovine reproduction and breeding.